I'm running XQuartz 2.7.9_rc2 on OS X 10.11.3 on a 27" iMac with dual displays. Usually, my X11-related windows are on my secondary display. "Displays have separate spaces" has been disabled due to other problems it introduces in relation to XQuartz.
Randomly, after the displays have gone to sleep my X11 windows cannot be found. When I engage Mission Control the X11 window (or windows) show up, but I cannot click on them or even drag them to a different display. The only solution is to go to Window and then click Zoom while holding down option. After that the window maximizes on my primary display; I then click + in the window bar and it returns back to my secondary display at its normal size and old position.
This has been happening for months.
*** This bug has been marked as a duplicate of bug 92653 ***